hi everyone,
I ran into this a while back, here is the soluton, it works great for me on 5.6
1. copy the template 40IBayAccess 
from /etc/e-smith/templates/etc/proftpd.conf 
 to /etc/e-smith/templates-custom/etc/proftpd.conf 
2. add this line 
$OUT .= " AllowChmod on\n"; 
above $OUT .= " AllowOverwrite on\n"; 
and below $OUT .= "<Directory  

 /home/e-smith/files/ibays/$key/*>\n"; 
3. expand the template /sbin/e-smith/expand-template  /etc/proftpd.conf 
you are done. this allows chmod capabilites for every ibay that you create.